I've purchased 3 Nitro's so far, the first was a 2007 SLT 4x4 for my wife to replace her Honda CRV, and I liked it so much that I sold my Toyota Sequoia with its V8 engine, and got myself the 2007 Nitro R/T 4x4. So, I have direct experience with both the 3.7L V6 Nitro with an automatic 4 speed transmission, and the 4.0L V6 Nitro with the 5 speed automatic trans. In my opinion, there is a huge difference in performance between the two vehicles, and I would never consider owning the 3.7L V6 Nitro with the 4 speed automatic, unless drastic modifications were done to it. The 3.7L V6 with 4 speed automatic not only performs much worse than the 4.0L V6, but the 3.7L V6 also gets worse gas mileage. I have no experience with the 6 speed manual transmission Nitro's, but think that it would make a big difference, unfortunately, not many manual transmission Nitro's were produced, compared to the automatic transmission models.
I have towed heavy trailers with my R/T Nitro, and it had no problem towing 5,000 lbs or more up steep hills and mountain roads, and only on the steepest grades did my speed dip below 55mph. So, IMHO, yes, there is a significant difference in the performance of the 3.7L V6, when compared to the 4.0L V6 Nitro models.
That being said, it is probably easier to improve the performance of the 3.7L V6, than it is to boost the HP of the already high performance 4.0L V6 in the R/T and later models of the Nitro. So if you already have the 3.7L V6 model of Nitro, do what Scar0 has done to improve his performance, and I'm sure you will be happy with the results.